Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region

Abstract

Background: The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. Methods: We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System, building on methods developed by the ARTIC network. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. Results: We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belonged to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. Conclusions: We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.

Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants

“…Complete consensus viral genomes are required to perform viral lineage tracking for genomic epidemiology. We obtained complete consensus SARS-CoV-2 genomes (breadth of coverage > 99%) from 7 out of 22 samples (31%), while large-scale patient sequencing efforts have for example obtained genomes for ∼80% of samples [31]. Only samples with RT-qPCR Ct-values < 33 (∼25 gc/uL) yielded complete consensus genomes ( Fig 1d ), but we also recovered at least one genome using each of our three extraction methods.…”

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients

“…Other approaches have included random primer metagenomic sequencing (sequence-independent single primer amplification [SISPA]) or metagenomic sequencing with spiked primer enrichment (MSSPE) to identify SARS-CoV-2 using mNGS methods with a limited sample size (2,3). Most studies have applied an amplicon-based approach to detect and sequence SARS-CoV-2 directly from specimens (1,2,(4)(5)(6)(7).…”

Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens

“…Using the cartridge for detection of SARS-CoV-2 variants we evaluated clinical samples from Johns Hopkins Hospital (JHH) as well as extracted RNA from B.1.1.7 and B.1.351 variants. All samples were previously classified by sequencing using the ARTIC protocol 31 To assess performance of the respiratory pathogen panel cartridges, we tested clinical swab eluates (n = 116) and passive drool saliva (n = 14). As a comparator assay, samples were first assessed with a benchtop assay adapted from the CDC recommended protocol (Supplementary Fig.…”

“…Testing of SARS-CoV-2 variants used RNA from clinical samples extracted using a chemagic 360 instrument (PerkinElmer) with clades of each sample previously characterized by sequencing 31 . 2 µL of extracted RNA was mixed with 150 µL magnetic bead binding buffer following by loading into the sample port of the cartridge.…”